Elastic net regularized regression for time-series analysis of plasma metabolome stability under sub-optimal freezing condition

Scientific Reports
Gerard Bryan Gonzales, Sarah De Saeger

Abstract

In this paper, the stability of the plasma metabolome at -20 °C for up to 30 days was evaluated using liquid chromatography-high resolution mass spectrometric metabolomics analysis. To follow the time-series deterioration of the plasma metabolome, the use of an elastic net regularized regression model for the prediction of storage time at -20 °C based on the plasma metabolomic profile, and the selection and ranking of metabolites with high temporal changes was demonstrated using the glmnet package in R. Out of 1229 (positive mode) and 1483 (negative mode) metabolite features, the elastic net model extracted 32 metabolites of interest in both positive and negative modes. L-gamma-glutamyl-L-(iso)leucine (tentative identification) was found to have the highest time-dependent change and significantly increased proportionally to the storage time of plasma at -20 °C (R2 = 0.6378 [positive mode], R2 = 0.7893 [negative mode], p-value < 0.00001). Based on the temporal profiles of the extracted metabolites by the model, results show only minimal deterioration of the plasma metabolome at -20 °C up to 1 month. However, majority of the changes appeared at around 12-15 days of storage. This allows scientists to better plan logistics and stor...Continue Reading

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Citations

May 7, 2019·Frontiers in Plant Science·Afef MarzouguiSindhuja Sankaran
May 3, 2019·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Deshayne B FellKumanan Wilson

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Methods Mentioned

BETA
PCA
nuclear magnetic resonance

Software Mentioned

Glmnet
MEBA
MATLAB©
R
LASSO
COVAIN
Progenesis QI
Excel
caret
Metabolomics

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